6NJG: Ubiquitin Variant

Ubiquitin Variant in Complex with Ubiquitin Interacting Motif. Determined by X-ray diffraction at 2.35 Å resolution. Released 6 Mar 2019.

Method: X-ray diffraction
Resolution: 2.35 Å
Organisms: Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Homo sapiens
Chains: 2
Atoms: 726
Mol. weight: 12.57 kDa
Released: 6 Mar 2019

Explore 6NJG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NJG contains 5 α-helices and 5 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1-14	14

Chain C: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	22	1	1
α-helix	23-34	12
α-helix	38-40	3
β-strand	41-45	5	2
β-strand	48-49	2	2
α-helix	50-51	2
β-strand	55	1	1
α-helix	57-59	3
β-strand	68-71	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar protein sorting-associated protein 27	B	protein	24	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P40343 (AlphaFold model)
Polyubiquitin-B	C	protein	89	Homo sapiens	J3QS39 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>6NJG_1 Vacuolar protein sorting-associated protein 27 (chains B)
YPEDEEELIRKAIELSLKESRNSA

Sequence of entity 2 (C), FASTA

>6NJG_2 Polyubiquitin-B (chains C)
GGAAQPAMQIFVQTITVMRIALEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGMQLEDG
RTLSDYNIKRDSNLYLVSSLRSLRAGAAA

Primary citation

Dimerization of a ubiquitin variant leads to high affinity interactions with a ubiquitin interacting motif. Manczyk, N., Veggiani, G., Gish, G.D. et al. Protein Sci (2019) 28:848-856. DOI 10.1002/pro.3593 · PubMed

Other PDB entries of the same protein (UniProt P40343 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1VFY 1.15 Å, Phosphatidylinositol-3-phosphate binding fyve domain of VPS27P protein from…
1O06 1.45 Å, Crystal structure of the Vps27p Ubiquitin Interacting Motif (UIM)
3R42 1.87 Å, Crystal structure of the yeast vps23 UEV domain in complex with a vps27 PSDP peptide
2PJW 3.01 Å, The Vps27/Hse1 complex is a GAT domain-based scaffold for ubiquitin-dependent sorting
1Q0V Solution Structure of Tandem UIMs of Vps27
1Q0W Solution structure of Vps27 amino-terminal UIM-ubiquitin complex
2KDI Solution structure of a Ubiquitin/UIM fusion protein

Browse structure collections

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